Friday, June 30, 2017

“A bunch of elite cyclists have a microbiome that looks like this,” the way Petersen describes, fecal transplant expert and professor Elizabeth Hohmann from Massachusetts General Hospital told Gizmodo. “So what? Is that because of the foods they eat?” After all, it could be the lifestyle that makes their microbiome look the way it does, not the microbiome that makes them better performers. “There are associations, but not causal. The idea that [microorganisms like] Methanobrevibacter smithii or Prevotella will make you a better performer is ridiculous.”

and this

And the fact that Petersen felt better after a fecal transplant is an anecdote that could simply be the placebo effect in action.

and this

There’s always the chance that poop doping could be harmful, too. “There’s the risk of transmission of infections agents for sure,”

"The treatment helped her battle Lyme Disease, however, there was a downside."

No evidence exists that this treatment helped her battle Lyme disease.

"“I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible,”"

This is reported with no caveats when there should be plenty. This is almost certainly a incorrect interpretation by her.

"What’s worse, during graduate school Petersen had her digestive system tested and discovered that she was full of gram-negative pathogens. Common strains of the pathogens include E.coli and Salmonella."

Almost certainly this is also a misinterpretation. Most tests such as those by American Gut which she claimed to have done would not have been able to say if she had pathogenic versions of these bugs.

The results were astounding

This implies cause and effect which has not been shown.

It turns out that Petersen probably would not have been doing as well if she’d gotten a couch potato’s poop.

No evidence for this exists.

she already knows that it plays a critical part of muscle recovery.

I am deeply skeptical of this claim.

Besides creating flatulence, decreasing the amount of hydrogen in our gut increases the amount of calories that are extracted from food, a study published in PLos One suggests.

It is really great that they link to a paper thus trying to show there is evidence for a claim. Alas, the paper does not show what is claimed here. This paper is just about comparing abundance of different microbes in obese, anorexic and control patients. So to say they "suggest" that this papers shows this methanogen is involved in increasing the amount of calories extracted from food is misleading. The authors hypothesize that sure. So in one sense they "suggest" this but the way this is written implies they actually studied that, when they did not.

Here is some commentary on just some of what is wrong with the Post article.

"Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better"

No evidence has been presented anywhere that these microbes "allow them to perform better". At best, there may be evidence that elite athletes in this case have different microbes. That as far as I know has not been presented for the case here. Seems possible. But this of course does not mean that those microbes they have allow for better performance. There could be dozens of reasons why such athletes have differences in their micro biomes (e.g., diet, exercise, interactions all effect the microbiome).

Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.

Seriously? This basically is implying that she did a self fecal transplant that enhanced her performance and cured her Lyme disease. She is an N of 1. She did a fecal transplant and then some of her self assessed health changed. What about, say, the placebo effect? Or, how about - 100 other things changed in her life before and after the fecal transplant which could have affected her. Or maybe the antibiotics she claimed to have taken before the transplant did something? Ridiculous to make any claims about her self fecal transplant having any known impact.

Then there is this

“I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible,” she told Bicycling.

This is a pretty stunning claim. She had no microbes that help break down food before this? And she also had been infected by microbes from the lab where she worked? I don't buy either of these claims.

And what about

“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”

Referring to home fecal transplants. I mean, I am all for people doing really whatever they want at home. But they should do it with their eyes as wide open as their other parts. And that requires the full poop on fecal transplants. They have real and potential risks (e.g., see this). One can get pathogens from them. The transplant itself could have negative effects. And if one assumes the microbiome has major effects, then one might get other unwanted traits from the donor too. It is dangerous to promote self fecal transplants without discussing any of the possible risks.

Overall, I find this reporting by the Post to be dangerous. And no the one caveat in the article below is not enough

Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.

How about instead of "she is not convinced" saying "There is no evidence for any of her claims and this is snake oil". That would be more accurate.

Because the text has been changed in the Washington Post story I am posting the text here from the Denver Post version in case it gets updated too, so people can see the original.

-------------------------------
To be a professional cyclist, one must have guts, microbiologist Lauren Peterson says, and she doesn’t just mean that in the metaphorical sense. Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better, and if you don’t have it, well, there may soon be a way to get it.

“Call it poop doping if you must,” Peterson told Bicycling magazine last week about her research.

Peterson, a research scientist at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut, heads up an initiative called the Athlete Microbiome Project, in which she compares stool samples of elite cyclists to amateur bikers. Her findings strikingly shine a light on a handful of microorganisms that apparently separate the guts of elite athletes from average people.

The most important, perhaps, is Prevotella. Not typically found in American and European gut microbiomes, Prevotella is thought to play a role in enhancing muscle recovery.

“In my sampling, only half of cyclists have Prevotella, but top racers always have it,” she told Bicycling. “It’s not even in 10 percent of non-athletes.”

Peterson reports she hosts Prevotella in her own gut – but not naturally. In fact, she might be the first case of “poop doping,” thanks to a fecal transplant she administered herself three years ago. Her donor? Another elite athlete.

Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.

“I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible,” she told Bicycling.

But, she continued, “I couldn’t find a doctor who could help me” since in the United States, fecal transplants are only performed to treat serious cases of Clostridium difficile, a disease that causes chronic diarrhea. And so Peterson went rogue.

Peterson detailed her decision to perform the “risky” procedure on herself on the podcast “Nourish Balance Thrive” last year. She admitted to thinking it was a “bad idea” at first because if not done with proper screenings of both parties, it could worsen a person’s problems. But through chance, she came across a donor, an elite long-distance racer, who had his microbiome mapped and screened after a case of food poisoning, which showed he was otherwise healthy. So Peterson took antibiotics to wipe out her own gut bacteria and essentially performed a reverse enema.

“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”

Within a month, Peterson said, she began feeling better than she’d felt in years.

“I had more energy than I knew what to do with,” she told the same podcast last year. “Like everything just changed.”

More importantly for her life’s work, however, her own success with the fecal transplant gave her the idea to start the Athlete Microbiome Project, for which she rounded up 35 of her cycling friends, according to the Scientist magazine, to kick off her research.

Along with Prevotella, Peterson said she also identified another possibly performance-enhancing microbe called Methanobrevibacter archaea, which Peterson found to be more prevalent in the samples from elite athletes. This bacteria’s function is also opaque, however, Peterson told the Scientist, “it allows your entire gut microbiome to work more efficiently” by more effectively breaking down complex carbohydrates in the gut.

Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.

“What we’re learning is going to change a lot for cyclists as well as the rest of the population,” Petersen told Bicycling magazine. “If you get tested and you’re missing something, maybe in three years you’ll be able to get it through a pill instead of a fecal transplant. We’ve got data that no one has ever seen before, and we’re learning a lot. And I think I can say with confidence that bacterial doping . . . is coming soon.”

And the answer should be "We have no $(*#()$()@#)@# idea if this is a good idea". But instead the answer was hype, overselling, and some bad microbiology reporting.

Here are some parts I am not a fan of.

The results showed she was populated by 96% gram-negative pathogens so toxic that if they got into her blood stream they could kill her. “I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible.”

I doubt much off this. I don't think the American Gut project can say anything about pathogens nor do I think they do say this. My guess is this is a misinterpretation by the scientist here or more likely the reporter. Also I doubt the American Gut data could be used to say anything about picking up bugs in the lab.

She observed that Prevotella, a microorganism she received in her own transplant, is common amongst elite racers. “The more a person trains, the more likely they are to have Prevotella,” says Petersen. “In my sampling, only half of cyclists have Prevotella, but top racers always have it... it’s not even in 10% of non-athletes.”She is currently extracting Prevotella to understand what it is, and how to boost its abundance naturally or through a probiotic pill for athletes or aspiring athletes. What she already knows: Prevotella synthesize branch chain amino acids critical for muscle recovery.

This too has some dubious parts. Especially going from a correlation (althetes vs. Prevotella) to "how to boost its abundance." How about first showing that is has any effect?

Archeon are ancient microorganisms that have managed to survive for millions of years in hostile habitats like sulfur springs and deep in the ocean. They also live in the human digestive system, where they have specialized functions. Like Prevotella, Elite cyclists often have M. smithii, but it’s less common in amateur racers. That’s significant because M. smithii also appears to be a performance-enhancing microbe.

Well - no modern organisms are ancient, first of all. And no Archaea have not managed to survive for millions of years - they live and die and their lineages evolve. As far as I know, nobody has shown this organism is performance enhancing - I could not find anything in the literature about this. It is a nice model. But many models are nice and then are wrong.

And then there is this

As for actual poop doping…. fecal transplants are available, but not in the U.S. “If you have the money for the procedure, you can go to a clinic in the UK or the Bahamas,” says Petersen. “But you can’t choose your donor, and it’s a risky procedure. As with any transplant, your immune system could reject what you get. It’s not something you should take lightly. I did a lot of research, and I took a risk for sure.”

Umm - she is a single case study and there is no evidence I know of that her transplant let to any improvement in performance. Dangerous claims right here. Fecal transplants indeed have real risks. Encouraging people to use them for doping is dangerous.

And thus Bicycling Magazine is a recipient of the Overselling the Microbiome Award.